Abstract
Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using molecular dynamic (MD) and metadynamics simulations, we provide a comprehensive description of the conformational transitions of the enzyme after mutating serine to proline. Our results suggest that the serine plays a crucial role in maintaining the closed conformation of wild-type GK and the GMP recognition. On the contrary, the S→P mutant exhibits a stable open conformation and loses the ability of ligand binding, which explains its functional transition from the GK enzyme to the GK domain. Furthermore, the free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT GK is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant. In addition, the FEPs show that the S→P mutation can also leads to the mis-recognition of GMP, explaining the vanishing of catalytic activity of the mutant.
Highlights
Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation
The free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT guanylate kinase (GK) is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant
We further investigated the relationship between the conformational transitions and GMP binding in both WT and S35P GK by employing the bias-exchange metadynamics[23]
Summary
Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation. In the case of guanylate kinase (GK), the functional novelty is induced by a single (SRP) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. In the case of the guanylate kinase (GK) enzyme[3,4,5], functional novelty is observed in a single (SRP) mutation, leading to the conversion of the protein from a phosphoryl transfer kinase into a phosphorprotein interaction domain[6,7]. Johnston et.al[7] demonstrated that a single mutation (S35P) of GK enzyme would fundamentally alter the protein function and switch it from a phosphoryl transfer kinase into a phosphoprotein interaction domain to regulate spindle orientation. By comparing the difference between the crystal structures of GK enzyme[6,7,8,9] and GK domain[22], it can be observed that eight residues from the GK enzyme directly contact with the ligand and three residues (Ser35,Glu[70] and Asp101) more closely coordinate to the guanine ring of GMP, while the other five residues remain invariant from the GK enzyme to the GK domain
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